Crystallographic Computing System for Standard and Modulated Structures

Vaclav Petricek, Michal Dusek & Lukas Palatinus

Jana2006 is a crystallographic program focused to solution,
refinement and interpretation of difficult, especially modulated structures. It calculates structures
having up to three modulation vectors from powder as well as single crystal data measured with X-ray
or neutron diffraction. The input diffraction data can be unlimitedly combined, the combination of powder
neutron data with single crystal X-ray data being a typical example. The structure solution can be
done using the built-in charge flipping algorithm or by calling an external direct methods program.
Jana can handle multiphase structures (for both powder and single crystal data), merohedric
twins as well as twins with partial overlap of diffraction spots, commensurate and
composite structures. It contains powerful transformation tools for symmetry (group-subgroup relations),
cell parameters and commensurate-supercell relations. Wide scale of constrains and restrains is available
including a powerful rigid body approach and possibility to define a local symmetry affecting only part of
the structure. The latest development of Jana concerns magnetic structures.

July 25, 2008 The first
stable
version of Jana2006 for Windows.
This program is the successor of Jana2000. Currently only Windows version is available,
Unix version as well as manual are under development. The Stable version will be changed
occassionally, the everyday work will be immediately available in the Latest version.
Registered users will be informed about new Stable versions.
Jana2006 can be obtained in Download area.

July 22, 2008 New web page for Jana
contains all information about Jana2006 and the previous version Jana2000.
We have partially changed also download locations, please do not use old links.

December 28, 2007 Final version of Jana2000 -
see the Download area.
No further development is expected in Jana2000.

CookbookJana Cookbook cumulates examples from Jana workhops. The last version is always copied here together with input data.
Raw data for electron diffraction examples are provided separately due to their size.

STABLE versions are not frequently changed, registered users get information
about their releases. LATEST versions are changed frequently and contain the latest
development. FINAL versions are not further developed. BETA versions are pre-releases
of new major upgrades.

Installation

Jana2006 for Windows.
Execute janainst.msi and follow the instructions. Execute jana2006.exe and
check the version string in Tools->About Jana2006.

Jana2006 for Windows, old way of installation
from janainst.exe.
Follow the instructions for Jana2000. For the system environment variable
use the name JANA2006DIR instead of JANADIR.

Jana2006 for UNIX.
Unix version is not yet available.

Jana2000 for Windows.
Execute the self-extracting archive janainst.exe. Before the extraction
choose installation directory. After the extraction go to Control panel
- System - Advanced - Environment variables and set the system-wide
environment variable JANADIR to the name of the installation directory.
Go to Display Properties - Effects and make sure Clear type fonts
are not used for smoothing edges of screen fonts.
Execute jana2000.exe.
For upgrade execute the self-extracting archive janainst.exe and
choose the same installation directory where the original version of Jana2000
has been installed.

Jana2000 for UNIX, fresh installation.
Requisities: FORTRAN compiler, C compiler, SDK for X11.
Download jana2000Pack.exe and put it one level above the future
installation directory (for jana2000Pack.exe in directory xxx, the
installation directory will be xxx/jana2000). Start csh or tcsh,
execute `source jana2000Pack.exe' and follow instructions
of the installation procedure. No JANADIR is necessary if the installation
stays in the default directory.

Common troubleshooting for Windows.

Installation from janainst.exe: Make sure that JANADIR or JANA2006DIR
contains correct name of installation directory.

Installation from CD: Make sure that files copied from CD are not read-only.

Jana2000 cannot be used with Clear type fonts.

Installation directory should not be Desktop (too complicated pathname)
or flashdisk (too slow)

Installation from janainst.msi over older version installed from
janainst.exe: in most cases it runs normally. The installation procedure sets
automatically system environment variable JANA2006DIR but does not
define the user environment variable. In case of version mismatch please
ensure that the user variable JANA2006DIR is undefined.
In rare cases the installation
from janainst.msi leaves the original files unchanged. This can be recognized
in Tools->About where the version string is not updated after installation. In such case the
installation directory of Jana2006 should be deleted (keep copy of ini and hst file)
as well as the user or system environment variable JANA2006. Then repeat installation from
janainst.msi.

Common troubleshooting for UNIX.
Make sure SDK for X11 is installed, in most Linux distributions
only run-time libraries are present by default. The installed Jana
executable cannot be moved from the default installation directory
jana2000 without special arrangements.

Registration
Jana system is a freeware but we are interested who is using it. Registered
users are placed to our internal list and get e-mails
about major updates.

New registration: type your e-mail,
choose a password and submit the registration.

Changes of existing registration:
type your e-mail, password and submit. Forgotten
password can be sent to your e-mail address

Do not use precious passwords, this is not encrypted connection.

e-mail:

Password:

External Programs

Main parts of Jana are our own computer code. For some special functionalities
Jana can call external programs. Some of them are distributed with Jana, the others must be
downloaded from their web pages. The configuration of external programs is done through Tools -> Preferences.

Program

Description

www

Superflip

Program for solving structures by charge flipping.
Distributed with Jana and immediately available.

Programs for plotting crystal structures. It can be any program accepting CIF
as an input in command line, for instance Diamond, Atoms, Platon.
Available after download, installation and defining the path
in Tools->Preferences->Graphic viewer.

many possibilities

Ad hoc workshops on Jana

Ad hoc workshops are small two days workshops organized in Praha by authors of Jana software. A new workshop
is usually organized when we find an overlap in topics in the list of preliminary registrations for at least
five people. In such case the program details and the dates are discussed with participants and fixed.
Another participants can register for a workshop with fixed program and date up to 12-15 people.
Participants pay themselves all their expenses and they are expected to bring their own laptops with
Windows. However, we can lend one or two laptops to those who cannot
bring their own ones.
The registration fee is zero (in Czech Crowns). Workshop certificates
are issued by our skilled artists on demand.

Registration
By e-mail to Michal Dusek (dusek@fzu.cz). For workshops without fixed program or for
future not yet announced workshops please give a list of selected topics, rated by importance.
Although a workshop can usually have only four topics (one topic takes 1/2 of day) the number of
selected topics can be higher, it helps finding overlaps. Please indicate if you have already
experience with Jana software. New users should select the topic "INT1". Those who would like
to participate in an advanced workshop (without INT1) but don't have an experience with Jana should
make Example 1.1 and 2.1 of the
cookbook as a homework.

Development of Jana is continuously supported by Grant Agency of the Czech Republic and
Academy of Sciences of the Czech Republic. Thanks to this support we can make the
program freely available to everybody.

Program development is not possible without user feedback and interaction. Please contact us
with bug reports, feature suggestions and structure determination difficulties. We also provide
measurement of interesting samples in our laboratory.